Autapses in the Layer 2/3 volume

Analysis and visualization of neurons that form a synapse onto itself

Contents

Summary Presentation

Notebooks and datatables

autapse_checker_entire_synapse_table.ipynb notebook: a simple method to identify potential autapses from the Layer 2/3 synapse table (pni_synapses_v185.csv).

autapses_rm_nonneuronal.csv datatable: a human-curated (by me) data table that removed the vascular and glial cell ids. This resulted in a list of 27 potential neuronal autapses. The electron micrographs for each of these were manually checked in neuroglancer and 3 of the 24 were determined to be true autapses. The remaining 24 were due to segmentation errors or edge artifacts.

autapses_layer23_volume.ipynb notebook: analysis and visualization of the three true autapses as well as some example segmentation errors from the autapses_rm_nonneuronal.csv datatable.

Visualization examples

Autapse 3623767

In an inhibitory basket neuron (cell id 648518346349528994)

inhibitory basket neuron autapse

Autapse 3966225

In an excitatory pyramidal neuron (cell id 648518346349538718)

pyramidal neuron autapse

Autapse 5423743

In an excitatory pyramidal neuron (cell id 648518346349539853)

pyramidal neuron autapse

Segmentation error examples

Two dendritic spines in contact with one another

Two dendritic spines from the same neuron in contact with one another where the synapse is assigned to the neuron; however upon inspection of the electron micrographs in Neuroglancer, there is an axon passing between the two spines and the segmentation algorithm failed to assign the synapse to the axon.

segmentation error between two spines with an axon passing between

Nuclear membrane segmentation error

A nuclear membrane mis-segmented as a synaptic membrane. This particular example shows an invagination of the nuclear membrane that was interpreted by the segmentation algorithm as a synapse.

segmentation error where a nuclear membrane is assigned as a synapse

Neuronal primary cilia segmentation error

The anchoring filament of a neuronal primary cilia is mis-segmented as a synapse.

segmentation error where an anchoring filament of the neuronal primary cilia is assigned as a synapse